title: In silico determination and validation of baumannii acinetobactin utilization a structure and ligand binding site.
abstract: Acinetobacter baumannii is a deadly nosocomial pathogen. Iron is an essential element for the pathogen. Under iron-restricted conditions, the bacterium expresses iron-regulated outer membrane proteins (IROMPs). Baumannii acinetobactin utilization (BauA) is the most important member of IROMPs in A. baumannii. Determination of its tertiary structure could help deduction of its functions and its interactions with ligands. The present study unveils BauA 3D structure via in silico approaches. Apart from ab initio, other rational methods such as homology modeling and threading were invoked to achieve the purpose. For homology modeling, BLAST was run on the sequence in order to find the best template. The template was then served to model the 3D structure. All the models built were evaluated qualitatively. The best model predicted by LOMETS was selected for analyses. Refinement of 3D structure as well as determination of its clefts and ligand binding sites was carried out on the structure. In contrast to the typical trimeric arrangement found in porins, BauA is monomeric. The barrel is formed by 22 antiparallel transmembrane β -strands. There are short periplasmic turns and longer surface-located loops. An N-terminal domain referred to either as the cork, the plug, or the hatch domain occludes the β -barrel.
authors.affiliation: Department of Biology, Shahed University, Tehran-Qom Express Way, Tehran 3319118651, Iran.
authors.forename: Fatemeh
authors.initials: F
authors.lastname: Sefid
authors.forename: Iraj
authors.initials: I
authors.lastname: Rasooli
authors.forename: Abolfazl
authors.initials: A
authors.lastname: Jahangiri
mesh_terms: D040981:Acinetobacter baumannii / Q000737:chemistry* / Q000235:genetics / Q000472:pathogenicity; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D003198:Computer Simulation; D003428:Cross Infection / Q000235:genetics / Q000382:microbiology*; D015964:Gene Expression Regulation, Bacterial; D007501:Iron / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008565:Membrane Proteins / Q000096:biosynthesis / Q000737:chemistry* / Q000378:metabolism; D017434:Protein Structure, Tertiary
chemical_list: D001425:Bacterial Outer Membrane Proteins; D008024:Ligands; D008565:Membrane Proteins; D007501:Iron